The URL for Manager is http://gisserver.domain.com:6080/arcgis/manager/. Alternatively, you can open Manager from the operating system shortcut that is installed with ArcGIS for Server.
Opening Manager the first time
When you open Manager the first time, you'll be asked whether you want to create a new site or join an existing site. Creating a new site means you are just getting started and you want to add this machine as the first GIS server in your configuration. Joining an existing site means that you want to add this machine as a GIS server in an existing configuration. See the help topics below to learn what you'll need to do for the option you choose:
Logging in to Manager
After you've created the site, you must log in to Manager using your primary site administrator name and password that you provided during the site creation process. The first time you log in, the Username box displays the primary site administrator name to remind you of this.
Subsequent attempts to log in to Manager require either the primary site administrator name and password, or the name and password of a user to whom you have granted administrator or publisher privileges using the ArcGIS for Server security mechanisms. If you provide a user with publisher privileges, some actions in Manager are restricted as described in Publisher role support in Manager.
Securing your login credentials
When you log in to Manager, your credentials are encrypted before being sent to the server. However, it is still a best practice to configure SSL and connect to Manager using HTTPS when logging in from a machine outside your network. This way all communication between the client and the server is encrypted. See Enabling SSL on ArcGIS Server.
If you run Manager under SSL, be sure to change the Manager shortcut to use https instead of http. To do this, right-click the shortcut, click Properties, then modify the target URL so that it begins with https.